Showing : gcrma • reset
2
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494
views
Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 10 months ago by 68k • written 10 months ago by • 0
2
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3
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1.5k
views
Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
3
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4
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1.5k
views
gcrma problem with make.cdf.package
gcrma make.cdf.package affy
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 40
0
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1
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1.8k
views
Is GCRMA normalization possible with oligo?
oligo pd.moe430a gcrma affymetrix normalization
updated 5.9 years ago by • 0 • written 6.8 years ago by ★ 4.1k
0
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2
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1.2k
views
u133aaofav2 platform gcrma Normalization
u133aaofav2 annotation gcrma
6.3 years ago samane.khoshbakht • 0
0
votes
1
reply
905
views
Normalization large data set
normalization gcRMA
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
0
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1
reply
2.0k
views
gcrma background correction-saving output
cdf affy gcrma matchprobes affyio cdf affy gcrma matchprobes affyio
updated 6.8 years ago by 0 • written 18.9 years ago by ★ 2.2k
4
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3
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1.5k
views
GCRMA not working inside tryCatch block in R
gcrma simpleaffy error handling trycatch
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
0
votes
1
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2.2k
views
Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds while using GCRMA
gcrma wheatcdf cdf
updated 7.1 years ago by 68k • written 7.1 years ago by • 0
0
votes
8
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4.9k
views
error ReadAffy
Arabidopsis thaliana cdf affy gcrma PROcess oligo xps Arabidopsis thaliana cdf affy xps
updated 7.6 years ago by • 0 • written 11.7 years ago by ▴ 300
0
votes
2
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3.1k
views
gcrma error " 'Calloc' could not allocate memory"
gcrma error
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
0
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4
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3.6k
views
cdf file for Clariom S Human HT
gcrma
8.2 years ago kathleen.klein • 0
2
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7
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2.0k
views
Package gcrma: unused argument (validate = FALSE)
gcrma
updated 8.4 years ago by ★ 4.1k • written 8.4 years ago by ▴ 10
2
votes
3
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1.8k
views
unusal expression level values after normalization in Affymetrix microarray experiment
microarray gcrma affy hgu133a normalization
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 50
1
vote
8
replies
7.8k
views
Limma, SAM and Fold Change Calculation
affy limma gcrma siggenes
updated 8.5 years ago by 53k • written 18.3 years ago by ▴ 80
0
votes
2
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1.4k
views
error in gcrma function
gcrma
updated 8.6 years ago by ★ 4.1k • written 8.6 years ago by • 0
0
votes
1
reply
1.6k
views
single probe represent multiple genes?
gcrma microarray expressionset
updated 8.7 years ago by ▴ 840 • written 8.7 years ago by ▴ 20
0
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5
replies
2.8k
views
Problem installing XVector package
software error gcrma Xvector iranges
9.2 years ago • updated 9.1 years ago gary_smith • 0
2
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9
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4.0k
views
mta10cdf not installed Bioconductor
gcrma
updated 9.2 years ago by ▴ 40 • written 10.9 years ago by • 0
0
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2
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1.5k
views
GCRMA segmentation fault
gcrma segmentation fault segfault
updated 9.5 years ago by 68k • written 9.5 years ago by • 0
0
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0
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1.3k
views
Background correction arguments in R package GCRMA for microarray pre-processing analysis
gcrma normalization background correction microarray
9.9 years ago svlachavas ▴ 840
1
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4
replies
2.0k
views
AGI code in gcrma normalization output
gcrma software error annotation
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 40
1
vote
4
replies
2.0k
views
Trouble with gcrma, Segfault on background correction
gcrma affy
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 30
0
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1
reply
2.0k
views
Warnings after gcrma normalisation...
Microarray Normalization gcrma Microarray Normalization gcrma
updated 11.5 years ago by 68k • written 11.5 years ago by ▴ 150
1
vote
2
replies
2.2k
views
Help needed: extracting raw intensity values from Affy
probe affy gcrma probe affy gcrma
updated 11.8 years ago by ▴ 20 • written 11.8 years ago by ★ 1.5k
0
votes
0
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1.7k
views
How does one deal with spatial effects detected on single channel microarrays?
Microarray Normalization hu6800 affy gcrma marray nnNorm Harshlight Microarray hu6800
12.0 years ago Scott Robinson ▴ 130
0
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3
replies
8.1k
views
Error: cannot allocate vector of size
gcrma simpleaffy gcrma simpleaffy
updated 12.3 years ago by 68k • written 12.3 years ago by ▴ 50
0
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1
reply
1.6k
views
Using gcrma with \"Affymetrix GeneChip miRNA v1.0\" data
miRNA gcrma miRNA gcrma
updated 12.3 years ago by 21k • written 12.3 years ago by ★ 13k
1
vote
4
replies
7.9k
views
How is LIMMA actually calculating the average expression value
probe limma gcrma probe limma gcrma
updated 12.3 years ago by ▴ 150 • written 12.3 years ago by 53k
0
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0
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1.6k
views
How is LIMMA actually calculating the average expression value?
gcrma gcrma
12.4 years ago Garcia Orellana,Miriam ▴ 150
0
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7
replies
2.2k
views
affy code archeology: expresso behavior for liwong/invariantset
Regression gcrma Regression gcrma
updated 12.7 years ago by 68k • written 12.7 years ago by ★ 13k
0
votes
2
replies
3.3k
views
R 2.15.2 trouble
affy limma gcrma affy limma gcrma
updated 12.7 years ago by 25k • written 12.7 years ago by ★ 13k
0
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3
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3.2k
views
[GSVA] Segfault with GSVA
RNASeq Microarray Annotation gcrma convert GSVA RNASeq Microarray Annotation gcrma GSVA
updated 12.7 years ago by ▴ 230 • written 12.7 years ago by ★ 3.4k
0
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1
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1.5k
views
Can Bioconductor be used offline?
gcrma gcrma
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 10
0
votes
4
replies
1.8k
views
Affymetrix data double normalisation
Normalization gcrma Normalization gcrma
updated 13.1 years ago by 68k • written 13.1 years ago by ★ 13k
0
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5
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3.1k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 13.3 years ago by ▴ 930 • written 13.3 years ago by ▴ 150
0
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1
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1.4k
views
Best package or code to filter Affymetrix probes by present calls??
Normalization gcrma Normalization gcrma
updated 13.3 years ago by 68k • written 13.3 years ago by ▴ 150
0
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0
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1.5k
views
PROBLEM LOADING THE covdesc FILE IN SIMPLEAFFY
Normalization gcrma Normalization gcrma
13.3 years ago Garcia Orellana,Miriam ▴ 150
0
votes
9
replies
3.4k
views
gcrma problem while processing HuGene-1_0-st-v1 genechip from Affymetrix
Normalization gcrma Normalization gcrma
13.3 years ago suparna mitra ▴ 290
0
votes
5
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2.1k
views
Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf'
Microarray Normalization cdf gcrma Microarray Normalization cdf gcrma
updated 13.4 years ago by 68k • written 13.4 years ago by ▴ 30
0
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3
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1.7k
views
Building specific Ortoghonal contrasts in LIMMA
limma gcrma limma gcrma
updated 13.4 years ago by 53k • written 13.4 years ago by ▴ 150
0
votes
2
replies
11k
views
problems with "cannot allocate vector of size.."
Microarray gcrma Microarray gcrma
updated 13.6 years ago by ★ 13k • written 13.6 years ago by ▴ 70
0
votes
0
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1.4k
views
Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!
Cancer cdf probe affy gcrma AnnotationDbi Cancer cdf probe affy gcrma AnnotationDbi
13.6 years ago Benjamin Otto ▴ 830
0
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1
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1.3k
views
arrayQualityMetrics: expression or probe-level data?
Cancer gcrma Cancer gcrma
updated 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 20
0
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1
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1.1k
views
\'mirna20probe
miRNA affy gcrma miRNA affy gcrma
updated 14.0 years ago by 68k • written 14.0 years ago by ★ 13k
0
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2
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2.5k
views
Installing packages on R v2.13.2, OSX multiple warning messages
Annotation cdf probe affy gcrma Annotation cdf probe affy gcrma
updated 14.0 years ago by 68k • written 14.0 years ago by ★ 13k
1
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1
reply
1.9k
views
gcrma failed on mouse Gene 1.0 ST array
probe gcrma probe gcrma
updated 14.0 years ago by ★ 4.1k • written 14.0 years ago by ▴ 50
0
votes
2
replies
1.9k
views
Unable to read Affy Mouse Exon 1.0 ST array CEL file
Annotation cdf affy gcrma oligo Annotation cdf affy gcrma oligo
updated 14.2 years ago by ★ 3.9k • written 14.2 years ago by ▴ 60
0
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1
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1.4k
views
gcrma
affy gcrma affy gcrma
updated 14.3 years ago by ▴ 50 • written 14.3 years ago by ▴ 30
0
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1
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1.4k
views
fold change after gcrma()
gcrma convert gcrma convert
updated 14.3 years ago by ★ 4.3k • written 14.3 years ago by ▴ 40
406 results • Page 1 of 9
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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